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PubMed1992

The chirality of ground DNA knots and links.

The chirality of ground DNA knots and links is described and characterized in terms of color symmetry groups (CSG), i.e. color symmetry groups I and II, which correspond to topochirality (topological chirality) and topoachirality (topological achirality) which bear an uncanny resemblance to point groups I (proper) and point groups II (improper) used for testing geochirality (geometrical chirality) and geoachirality (geometrical achirality), respectively. By regarding these two crossing modes in mirror images as white and black vertices, DNA knots and links with minimal crossings can be mapped to vertex-bicolored graphs under a working hypothesis that DNA knots and links exist in ground states with minimal energy m0. The color symmetry group of a vertex-bicolored graph G is defined as the set of all permutations and permutation asymmetrizations of the vertices of G that preserve its topology (connectivity), where asymmetrization, denoted as (a), is the operation of changing vertices' colors, and a permutation followed by an (a) is a permutation asymmetrization. The color symmetry groups I contains only permutations, whereas color symmetry groups II comprise permutation asymmetrizations as well as permutations. Four DNA knots and links in nature are analyzed and tabulated consisely. In addition, the well-known figure-of-eight knot and Borromean rings are discussed in much the same way.

DNA↗
PubMed1986

Relation of branching angles to optimality for four cost principles.

The literature has suggested that branching angles depend on some principle of optimality. Most often cited are the minimization of lumen surface, volume, power and drag. The predicted angles depend on the principle applied, chi and alpha. Assuming flow o r chi, chi can be determined from r chi 0 = r chi 1 + r chi 2 when the radii of the parent (r0) major (r1) and minor (r2) daughters are known. The term alpha = r2/r1. Using different values for chi and alpha, we present graphs for the major and minor branching angles theta 1 and theta 2 and psi = theta 1 + theta 2 for each of the four optimization principles. Because psi is almost independent of alpha for values of chi and alpha found in 198 junctions taken from a human pulmonary artery, we are able to produce a plot of psi versus chi for each of the four principles on one graph. A junction can be provisionally classified as optimizing for a given principle if, knowing chi, the psi obs - psi pred is least for that principle. We find that this nomographic classification agrees almost perfectly with a previous classification based on a more exacting measure, the percent cost index I, where I = observed cost/minimum cost. We explain why this is to be expected in most but not all cases. First we generate a contoured percent cost surface of c = I - 100 around the optimally located junction, J, and superimpose a surface of equal angular deviations a = psi pred-psi obs. We find that c increases and a usually increases with distance from J as the actual junction moves along a straight line away from J. We then produce a plot of c versus a for two competing principles. A comparison of the principles demonstrates that, for most cases, a is smaller for the principle which has the smaller c value.

Blood Flow Velocity↗
PubMed1987

Minimal spanning tree analysis of biological structures.

A new approach to study order and disorder in biological membranes and more generally in biological structures is developed. It is based on a graph constructed on the set points representing the position of particles. From this graph, which is called the minimal spanning tree, it is possible to deduce two parameters, namely the average length m and the standard deviation sigma which are characteristic of the repartition to be studied. The use of a diagram involving both m and sigma makes it possible to determine the degree of order by taking a simple reading in the (m, sigma) plane.

Cell Membrane↗
PubMed1988

Quantization of directional properties in biological structures using the Minimal Spanning Tree.

A method that uses the Minimal Spanning Tree graph has previously been developed (Dussert et al., 1987, J. theor. Biol. 125, 317) in order to analyse the degree of order in biological structures. This graph is shown here to be very powerful in bringing out directional properties of biological structures which cannot be revealed by a simple visual examination. The method is illustrated by means of various computer simulations.

Computer Simulation↗
PubMed1992

Stone surface area determination techniques: a unifying concept of staghorn stone burden assessment.

The use of stone surface area measurements obtained from standard radiographs provides a more accurate and reproducible assessment of stone burden when reporting results and treatment recommendations for staghorn calculi. Techniques for determining stone surface area include use of graph paper, planimeter or computerized image analysis. The use of graph paper is inefficient while planimeters suffer from significant variation for areas less than 500 mm.2 (more than 5%). Computer image analysis is accurate, rapid and easiest to perform. Software programs compatible with microcomputers are readily available making assessment of stone surface area practical and inexpensive. Stone surface area showed close correlation to stone volume as measured by 3-dimensional computerized tomography (correlation coefficient 0.84, p = 0.005). Stone surface area determination enables more accurate reporting of treatment results and, thus, recommendations based upon stone burden. Comparison of data between institutions becomes more meaningful if stone surface area is used. Stone surface area also provides a useful basis to study and compare trends of treatment within a single institution.

Humans↗
PubMed1979

Male peak urinary flow rate: relationships to volume voided and age.

We performed 126 studies of replicate voiding in 7 individuals and 552 observations in normal, abnormal or treated male populations with a disposable device that measures peak flow and volume voided. These observations have led us to suggest that a voided volume of 150 ml. be used as the minimum acceptable volume for studies of male subjects in which peak flow is used to define normal versus abnormal voiding. At volumes greater than 150 ml. a straight line describes the relationship between volume voided and peak flow as accurately as the previously suggested hyperbolic curve. Increasing age of men again reveals progressive decrease in peak flow rate no matter what volume is voided. Comparison of peak flow rate, volume voided and age by 3-dimensional graphing was attempted but was found unsuccessful for clinical use. However, 3 biaxial linear graphs may be used to chart effectively the 3 parameters (age, volume and peak flow) and thereby judge normality or abnormality of peak flow rate for any age and volume voided.

Adolescent↗
PubMed1999

Non-linear qualitative signal processing for biological systems: application to the algal growth in bioreactors.

We present in this paper a qualitative method to validate and monitor the structure of a non-linear model with respect to experimental data, under some hypotheses. This method is broadly independent of the analytical formulation of the model, and depends only on the qualitative structure (the signs of the Jacobian matrix). The temporal sequences of the extrema of a filtered experimental signal are compared with the transitions allowed by a graph. In particular, we show that the usual moving average of the outputs follows this transition graph. We apply this method to compare models of algal growth in a bioreactor with experimental data.

Bioreactors↗
PubMed1998

A masked randomized comparison of oral and vaginal administration of misoprostol for labor induction.

OBJECTIVE: To test the null hypothesis that administering misoprostol orally or vaginally will result in no difference in time to vaginal birth, and to determine whether different frequencies of tachysystole and hyperstimulation are associated with route of administration. METHODS: Two hundred six women after 37 completed weeks' gestation who presented with an indication for induction were randomly assigned to receive misoprostol (50 microg) either orally or vaginally every 4 hours as needed to induce labor. Placebo use and allocation concealment accomplished blinding until data analysis was completed. Sample size was calculated to allow a two-tailed alpha of .05 and power (1-beta) of 80%. All fetal heart rate and uterine activity graphs were classified according to Curtis' criteria before induction groups were unmasked. RESULTS: Analysis involved 104 women in the oral group and 102 in the vaginal group. The mean time (+/-standard deviation) to vaginal birth with oral misoprostol was 1072 (+/-593) minutes compared with 846 (+/-385) minutes with the vaginal protocol (P=.004). There were no significant differences in cesarean rate, epidural use, or neonatal outcomes. More frequent tachysystole for 20 minutes (P < .01) and hyperstimulation (P < .04) were observed with vaginal misoprostol. No neonatal asphyxia occurred in either group. CONCLUSION: Misoprostol effectively induces labor, given orally or vaginally. There is a shorter interval to vaginal birth with vaginal application; however, the more frequent occurrence of fetal heart rate graph abnormalities in this group suggests that, until the optimal dosing interval for vaginal use is determined, the preferred route of misoprostol administration might be oral.

Abortifacient Agents, Nonsteroidal↗
PubMed1996

TongueTwister: an integrated program for analyzing lickometer data.

The analysis of lickometer data is often rendered prohibitively tedious by the large volume of data generated by the typical experiment. TongueTwister is an integrated program for the rapid and automatic analysis, presentation, and summary of long- and medium-access data collected by lickometers or of brief-access data collected by multi-bottle lickometers such as the DiLog Instruments MS80. The program was written in C+2 for Macintosh computers, and analyzes data collected by MS-DOS PCs. It takes advantage of the Macintosh user interface to provide quick and convenient output from all the files of a single experimental session, and to export the data to third-party statistical software or other documents. It can batch-process data files by automatically opening and analyzing all the files in a directory; thus, the user can employ directories as a simple database for organizing experimental groups. When a lickometer data file is opened, a textual summary, a raster plot of the lick pattern, the cumulative licks, the lick rate, a histogram of inter-lick intervals, and a breakdown of the session by fractions are automatically calculated and displayed. When an MS80 brief-access file is opened, the lick pattern for each tube presentation and a textual summary of the mean values derived for each tube are automatically displayed. If a directory of files is opened, the mean values derived across all the individual files are calculated and graphed. Analysis parameters can be tailored to the investigator's liking. Tables or graphs can be saved to disk, or copied and pasted into other Macintosh programs for additional analysis. The program may also be used for general-purpose analysis of periodic event records.

Animals↗
PubMed2003

Computerized diagnostic decision support system for the classification of preinvasive cervical squamous lesions.

Previous studies have revealed considerable interobserver and intraobserver variation in the histological classification of preinvasive cervical squamous lesions. The aim of the present study was to develop a decision support system (DSS) for the histological interpretation of these lesions. Knowledge and uncertainty were represented in the form of a Bayesian belief network that permitted the storage of diagnostic knowledge and, for a given case, the collection of evidence in a cumulative manner that provided a final probability for the possible diagnostic outcomes. The network comprised 8 diagnostic histological features (evidence nodes) that were each independently linked to the diagnosis (decision node) by a conditional probability matrix. Diagnostic outcomes comprised normal; koilocytosis; and cervical intraepithelial neoplasia (CIN) I, CIN II, and CIN III. For each evidence feature, a set of images was recorded that represented the full spectrum of change for that feature. The system was designed to be interactive in that the histopathologist was prompted to enter evidence into the network via a specifically designed graphical user interface (i-Path Diagnostics, Belfast, Northern Ireland). Membership functions were used to derive the relative likelihoods for the alternative feature outcomes, the likelihood vector was entered into the network, and the updated diagnostic belief was computed for the diagnostic outcomes and displayed. A cumulative probability graph was generated throughout the diagnostic process and presented on screen. The network was tested on 50 cervical colposcopic biopsy specimens, comprising 10 cases each of normal, koilocytosis, CIN I, CIN II, and CIN III. These had been preselected by a consultant gynecological pathologist. Using conventional morphological assessment, the cases were classified on 2 separate occasions by 2 consultant and 2 junior pathologists. The cases were also then classified using the DSS on 2 occasions by the 4 pathologists and by 2 medical students with no experience in cervical histology. Interobserver and intraobserver agreement using morphology and using the DSS was calculated with kappa statistics. Intraobserver reproducibility using conventional unaided diagnosis was reasonably good (kappa range, 0.688 to 0.861), but interobserver agreement was poor (kappa range, 0.347 to 0.747). Using the DSS improved overall reproducibility between individuals. Using the DSS, however, did not enhance the diagnostic performance of junior pathologists when comparing their DSS-based diagnosis against an experienced consultant. However, the generation of a cumulative probability graph also allowed a comparison of individual performance, how individual features were assessed in the same case, and how this contributed to diagnostic disagreement between individuals. Diagnostic features such as nuclear pleomorphism were shown to be particularly problematic and poorly reproducible. DSSs such as this therefore not only have a role to play in enhancing decision making but also in the study of diagnostic protocol, education, self-assessment, and quality control.

Bayes Theorem↗
PubMed1999

How to select patients for high-energy transurethral microwave thermotherapy.

OBJECTIVES: To assist urologists in selecting patients for high-energy transurethral microwave thermotherapy (TUMT) on the basis of baseline characteristics. METHODS: Two hundred forty-seven patients with lower urinary tract symptoms and benign prostatic hyperplasia were treated with high-energy TUMT using the Prostatron device, software version 2.5. To evaluate outcome at 26 weeks, the World Health Organization response evaluation criteria were used. Multiple logistic regression models were created to identify the predictive value of baseline parameters and total amount of energy used. In addition, receiver operating characteristic curve and the best cutoff point for the prediction of a good response of each criterion under the condition of equal "costs" of misclassification to cases and noncases were calculated. RESULTS: For each of the three response evaluation criteria, graphs are presented to determine whether high-energy TUMT using the Prostatron can be justified. Only the total amount of energy delivered by the device has a major impact in all three criteria used. CONCLUSIONS: Graphs have been constructed from our analysis to assist urologists in making clinical recommendations for treatment on the basis of the expected outcome when using high-energy TUMT.

Aged↗
PubMed2003

Stoichiometric design of metabolic networks: multifunctionality, clusters, optimization, weak and strong robustness.

Starting from a limited set of reactions describing changes in the carbon skeleton of biochemical compounds complete sets of metabolic networks are constructed. The networks are characterized by the number and types of participating reactions. Elementary networks are defined by the condition that a specific chemical conversion can be performed by a set of given reactions and that this ability will be lost by elimination of any of these reactions. Groups of networks are identified with respect to their ability to perform a certain number of metabolic conversions in an elementary way which are called the network's functions. The number of the network functions defines the degree of multifunctionality. Transitions between networks and mutations of networks are defined by exchanges of single reactions. Different mutations exist such as gain or loss of function mutations and neutral mutations. Based on these mutations neighbourhood relations between networks are established which are described in a graph theoretical way. Basic properties of these graphs are determined such as diameter, connectedness, distance distribution of pairs of vertices. A concept is developed to quantify the robustness of networks against changes in their stoichiometry where we distinguish between strong and weak robustness. Evolutionary algorithms are applied to study the development of network populations under constant and time dependent environmental conditions. It is shown that the populations evolve toward clusters of networks performing a common function and which are closely neighboured. Under changing environmental conditions multifunctional networks prove to be optimal and will be selected.

Algorithms↗
PubMed2003

Identification of all steady states in large networks by logical analysis.

The goal of generalized logical analysis is to model complex biological systems, especially so-called regulatory systems, such as genetic networks. This theory is mainly characterized by its capacity to find all the steady states of a given system and the functional positive and negative circuits, which generate multistationarity and a cycle in the state sequence graph, respectively. So far, this has been achieved by exhaustive enumeration, which severely limits the size of the systems that can be analysed. In this paper, we introduce a mathematical function, called image function, which allows the calculation of the value of the logical parameter associated with a logical variable depending on the state of the system. Thus the state table of the system is represented analytically. We then show how all steady states can be derived as solutions to a system of steady-state equations. Constraint programming, a recent method for solving constraint satisfaction problems, is applied for that purpose. To illustrate the potential of our approach, we present results from computer experiments carried out on very large randomly-generated systems (graphs) with hundreds, or even thousands, of interacting components, and show that these systems can be solved using moderate computing time. Moreover, we illustrate the approach through two published applications, one of which concerns the computation times of all steady states for a large genetic network.

Arabidopsis↗
PubMed2002

Deciphering Arabidopsis thaliana gene neighborhoods through bibliographic co-citations.

In the framework of genome annotation, scientific literature is obviously the major source of biological knowledge. The aim of the work described in this paper is to exploit this source of data for the model plant Arabidopsis thaliana. The first step has consisted in constituting a relevant bibliographic references dataset for plant genomic research. Genes co-citations have then been systematically annotated in this reference dataset, starting from the simple idea that if genes are cited in the same publication, they must probably share some related functional properties. In order to deal with the synonymous gene name problem, a gene name reference list has been constituted starting from A. thaliana SwissProt entries. This list was used to build clusters of co-cited genes by a single linkage procedure such that any gene in a given cluster possesses at least one co-cited partner in the same cluster. Analysis of the clusters demonstrate the biological consistency of this approach, with only very few fortuitous links. As an example, a cluster including genes related to flowering time is more deeply described in the paper. Finally, a graphical representation of each cluster was performed, which provides a convenient way to retrieve the genes (the nodes of the graphs) and the references in which they were co-cited (the edges of the graphs). All the results can be accessed at the URL http://chlora.Igi.infobiogen.fr:1234/bib_arath/.

Arabidopsis↗
PubMed1997

Analysis of the forces developed during obturation: warm vertical compaction.

The aim of this work was to measure and analyze the forces applied by endodontists during an obturation. This was achieved by devising a system of force transducers linked to acquisition software. The software allowed us to study the obturation forces in real time or to store them. In this initial study, the forces developed by endodontists and students during a warm vertical compaction were analyzed. The vertical and frontware backware horizontal direction forces were first stored. Graphs of the compaction forces were then generated, permitting the analysis of the obturation method. Indeed, two cases of obturation failure were analyzed from these graphs. The mean values for the vertical forces applied by the endodontists and students were, respectively, 2.5 +/- 0.4 kg and 1.9 +/- 0.9 kg; the mean values for the lateral forces were, respectively, 0.85 +/- 0.2 kg and 1.4 +/- 0.6 kg. This device permits the analysis of compaction forces and may thus be highly useful in obtaining improvements in obturation techniques.

Analysis of Variance↗
PubMed1980

Three-dimensional perspective of U.S. cancer mortality.

Data from U.S. death certificates, 1950--77, can now be displayed as computer-generated three-dimensional graphs. The results provide a panoramic view of the rise and fall in cancer rates by age, sex, and calendar year for Whites and non-Whites. Sample graphs depict the rising rates for lung cancer, the falling rates for stomach cancer, the relatively constant rates for breast cancer, and the dramatic change in rates for childhood leukaemia.

Adolescent↗
PubMed1995

The effect of phenylephrine on Müller muscle. A blepharogram study of eyelid motion.

PURPOSE: The blepharogram technique is used to study the effect of a drug on blinking. The authors show that ocular instillation of phenylephrine, a stimulant of Müller muscle of the eyelid, accelerates the up phase of the blink. METHODS: Motion of a tiny search coil glued to the eyelid moving in a weak magnetic field modifies an induced alternating current which is amplified and used to display the position of the upper eyelid in degrees on the ordinate of a graph with time in milliseconds on the abscissa. The graph is called a blepharogram. Blepharogram studies and individual blink analysis show the effect of phenylephrine on eyelid motion (blinking). RESULTS: Instillation of phenylephrine accelerated the up phase of the blink in all ten experimental subjects. In 65% of subjects, phenylephrine also produced or increased newly described N and M blepharogram patterns. CONCLUSION: This is the first instrumental detection of the effect of a pharmacologic agent on eyelid motion. The blepharogram technique provides insight into eyelid physiology and can be used to study any neuromuscular condition that affects eyelid motion.

Adult↗
PubMed1990

Interindividual comparability of blood glucose alterations after meals of complex carbohydrates.

Young male and female probands underwent an DGTT (oral glucose tolerance test) using a glucose load of 1 g/kg b.wt. The alterations in blood glucose levels were checked and plotted by a Biostator. A week later groups of those probands were fed an isocaloric meal of complex CH, namely either potatoes, noodles or white bread. The resulting BG curves were also checked by a Biostator. It turned out that: 1. the shapes of the BG curves after glucose load were not interindividually comparable. 2. there was neither a similarity of the shapes of the BG curves within the groups after any of the different CH levels. 3. But if one compares the shape of the BG curves after glucose load and after a meal of any of the complex CH of one and the same person, there is a striking similarity in those curve shapes. The differences between them lie just in the mostly lower BG values of the curves after CH meals compared with those after glucose load. 4. Therefore the resulting graph of both of those curves is in all observed cases a straight line with a probability better than 0.001, called OGTT-calibrating resulting graph.

Adult↗

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